| Antibodies |
| Anti-phospho-PPARγ (Ser112) antibody |
Millipore |
Cat# 04-816 RRID: AB_10563102 |
| Anti-PPARγ antibody |
Cell Signaling Technology |
Cat# 2443 RRID: AB_823598 |
| Anti-β-ACTIN antibody |
Sigma |
Cat# A1978 RRID: AB_476692 |
| Anti-FLAG antibody |
Sigma |
Cat# F1804 RRID: AB_262044 |
| Anti-PLIN1 antibody |
Fitzgerald Industries International |
Cat# 20R-PP004 RRID: AB_1288416 |
| Anti-GFP antibody |
Abcam |
Cat# ab13970 RRID: AB_300798 |
| Anti-GSTM1 antibody |
Santa Cruz Biotechnology |
Cat# sc-517262 RRID: N/A |
| Anti-GPX3 antibody |
R&D Systems |
Cat# AF4199 RRID: AB_2112276 |
| Anti-HISTONE H3 antibody |
Cell Signaling Technology |
Cat# 4499 RRID: AB_10544537 |
| Anti-AhR antibody |
Enzo Life Sciences |
Cat# BML-SA210, RRID:AB_10540536 |
| Alexa Fluor 488 goat anti-chicken secondary antibody |
Invitrogen |
Cat# A-11039 RRID: AB_142924 |
| Alexa Fluor 647 goat anti-guinea pig secondary antibody |
Invitrogen |
Cat# A-21450 RRID: AB_141882 |
| PerCP/Cyanine5.5 anti-mouse CD45 antibody |
Biolegend |
Cat# 103132 RRID: AB_893340 |
| PerCP/Cyanine5.5 anti-mouse CD31 antibody |
Biolegend |
Cat# 102420 RRID: AB_10613644 |
| PE anti-mouse CD140b (PDGFRβ) antibody |
Biolegend |
Cat# 136006 RRID: AB_1953271 |
| APC anti-mouse Ly6C antibody |
Biolegend |
Cat# 128016 RRID: AB_1732076 |
| FITC anti-mouse CD9 antibody |
Biolegend |
Cat# 124808 RRID: AB_1279321 |
| BV421 anti-mouse CD26 (DPP4) antibody |
BD Biosciences |
Cat# 740021 RRID: AB_2739793 |
| Chemicals, Peptides, and Recombinant Proteins |
| Collagenase D |
Roche |
Cat# 11088882001 |
| RBC lysis buffer |
eBioscience |
Cat# 00-4300-54 |
| Lipofectamine LTX |
ThermoFisher Scientific |
Cat# 15338100 |
| Polybrene |
Sigma |
Cat# TR-1003 |
| DMEM/F12 GlutaMAX |
Life Techonologies |
Cat# 10565042 |
| DMEM |
Cellgro |
Cat# 10-014-CV |
| Insulin |
Sigma |
Cat# I6634 |
| IBMX |
Sigma |
Cat# I7018 |
| Dexamethasone |
Sigma |
Cat# D4902 |
| Lipopolysaccharides |
Sigma |
Cat# L3024 |
| Indoxyl sulfate potassium salt |
Sigma |
Cat# I3875 |
| CH223191 |
Sigma |
Cat# C8124 |
| Oil Red O |
Sigma |
Cat# O0625 |
| TRIzol |
Invitrogen |
Cat# 15596018 |
| Power SYBR Green |
Life Technologies |
Cat# 4368708 |
| Image-iT Fx Signal Enhancer |
Invitrogen |
Cat# I36933
|
| Prolong Anti-Fade mounting reagent with DAPI |
Life Technologies |
Cat# P36931
|
| Pierce IP lysis buffer |
ThermoFisher Scientific |
Cat# 87787 |
| Protease Inhibitor Cocktail |
Sigma |
Cat# P8340 |
| Phosphatase Inhibitor Cocktail |
Sigma |
Cat# P5726&P0044 |
| Protein G Sepharose 4 Fast Flow beads |
GE Healthcare Bio-sciences |
Cat# 17-0618-01 |
| Pierce IgG elution buffer |
ThermoFisher Scientific |
Cat# 21004 |
| RIPA Lysis Buffer System |
Santa Cruz Biotechnology |
Cat# sc-24948A |
| PVDF membrane |
Millipore |
Cat# IPFL00010 |
| Ammonium Hydrogencarbonate (Ammonium Bicarbonate) |
FUJIFILM Wako Chemical Corporation |
Cat# 018-21742 CAS RN: 1066-33-7 |
| cOmplete Tablets, Mini EDTA-free, EASYpack protease inhibitor cocktail |
Roche |
Cat# 04 693 159 001 |
| L-Cysteine |
FUJIFILM Wako Chemical Corporation |
Cat# 039-20652 CAS RN: 52-90-4 |
| DL-Dithiothreitol, >=98% (HPLC), >=99.0% (titration) |
Sigma |
Cat# D0632-1G CAS RN: 3483-12-3 |
| Ethyl Acetate |
FUJIFILM Wako Chemical Corporation |
Cat# 057-03371 CAS RN: 141-78-6 |
| Iodoacetamide |
Sigma |
Cat# I6125-25G CAS RN: 144-48-9
|
| Lysyl Endopeptidase Mass Spectrometry Grade |
FUJIFILM Wako Chemical Corporation |
Cat# 125-05061 |
| Sodium Deoxycholate |
FUJIFILM Wako Chemical Corporation |
Cat# 190-08313 CAS RN: 302-95-4 |
| Sodium N-Dodecanoylsarcosinate (Sodium N-Lauroyl Sarcosinate) |
FUJIFILM Wako Chemical Corporation |
Cat# 192-10382 CAS RN: 137-16-6 |
| Trifluoroacetic Acid Optima LC/MS |
ThermoFisher Scientific |
Cat# A116-50 CAS RN: 76-05-1 |
| Sequencing Grade Modified Trypsin |
Promega |
Cat# V5113 |
| Trizma Hydrochloride Solution, pH 9.0, 1 M |
Sigma |
Cat# T2819-100ML CAS RN: 77-86-1, Trizma base |
| ZipTip C18 Pipette Tips with 0.6 μL C18 resin |
Millipore |
Cat# ZTC18S096 |
| Trametinib |
Sellecchem |
Cat# S2673 |
| Critical Commercial Assays |
| NEBNext Poly(A) mRNA Magnetic Isolation Module |
New England Biolabs |
Cat# E7490 |
| NEBNext Ultra II RNA Library Prep Kit for Illumina |
New England Biolabs |
Cat# E7770 |
| RNeasy Mini Kit |
Qiagen |
Cat# 5805 |
| RNAqueous micro RNA Isolation Kit |
ThermoFisher Scientific |
Cat# AM1931 |
| M-MLV Reverse Transcriptase |
Invitrogen |
Cat# 28025-013 |
| GSH/GSSG Ratio Detection Assay Kit II |
Abcam |
Cat# ab205811 |
| Pierce BCA Protein Assay Kit |
ThermoFisher Scientific |
Cat# 23227 |
| Pierce High pH Reversed-Phase Peptide Fractionation Kit |
ThermoFisher Scientific |
Cat# 84868 |
| DCFDA/H2DCFDA cellular ROS Assay Kit |
Abcam |
Cat# ab113851 |
| Deposited Data |
| RNA-seq dataset |
This paper |
GEO Accession viewer: GSE165600
|
| Mass spectrometry dataset |
This paper |
ProteomeXchange: PXD023829 |
| Experimental Models: Cell Lines |
| Phoenix cell |
ATCC |
Cat# CRL-3213 RRID: CVCL_H716 |
| Experimental Models: Organisms/Strains |
| Mouse: B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J |
The Jackson Laboratory |
JAX 007676 |
| Mouse: B6.Cg-Tg(tetO-cre)1Jaw/J |
The Jackson Laboratory |
JAX 006234 |
| Mouse: C57BL/6-Tg(Pdgfrb-rtTA)58Gpta/J |
The Jackson Laboratory |
JAX 028570 |
| Mouse: TRE-Pparg2
|
Shao et al., 2018 |
N/A |
| Oligonucleotides |
| A full list of qPCR primers, see Table S5
|
This paper |
N/A |
| Recombinant DNA |
| psPAX2 |
Addgene |
Cat# 12260 |
| pMD2.G |
Addgene |
Cat# 12259 |
| LentiCRISPR V2 |
Addgene |
Cat# 52961 |
| Software and Algorithms |
| GraphPad Prism version 8.0 |
GraphPad Software, Inc |
https://www.graphpad.com
|
| FlowJo version 10.6.1 |
FlowJo, LLC |
https://www.flowjo.com
|
| ImageJ |
NIH |
https://imagej.nih.gov/ij/
|
| QIAGEN Ingenuity Pathway Analysis (Qiagen IPA) |
Qiagen |
https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/
|
| ClustVis |
Metsalu and Vilo, 2015 |
https://biit.cs.ut.ee/clustvis/
|
| Proteome Discoverer 2.4 |
ThermoFisher Scientific |
https://www.thermofisher.com/jp/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html
|
| Spectronaut |
Biognosys AG |
https://biognosys.com/shop/spectronaut
|
| HISAT2 |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/Rhisat2.html
|
| featureCounts |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/Rsubread.html
|
| trimgalore |
GitHub |
https://github.com/FelixKrueger/TrimGalore
|
| R version 4.1.2 |
|
https://cran.r-project.org/bin/windows/base/
|
| Other |
| High fat diet |
Research Diets |
Cat# D12492i |
| Doxycycline high fat diet |
Bio-Serv |
Cat# S5867 |
